First, every player makes errors, and 99.9% is not a realistic number by any stretch, especially given some of the throws that have to be made from in the hole and on the run and at awkward angles. But granted the throws have to be accurate close to every time. But here are things you are missing:
1. Most errors at SS are fielding errors. The throw doesn't matter if a player is less of a fielder.
2. What is "catchable" on a throw to first base isn't dependent on a deadly accurate throw to the chest. A throw at the shoes or a little over the head, or a few feet down the line one way or the other is still an easy catch for a 1st baseman. And even most throws in the dirt are still catchable, or a throw a 1st baseman has to jump a little for will work if it gets there early enough for him to come down before the runner gets there.
3. The SS has to cover more ground than every other infielder, so range is a huge factor. If one player is slightly more accurate throwing the ball, but he can't get to balls in the hole or up the middle as well as another player, and he has less arm strength to make those throws, he isn't going to be as good at the position.
4. Instincts are a huge factor at SS - more so than any position next to catcher. He is involved more than any other position player except catcher.
Again, I'm not talking about a massive difference in accuracy. I'm talking about a slight difference that when put in the context of the overall skillset is not enough to keep the more athletic, better fielding, more instinctual player off the field.
